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1.
CPT Pharmacometrics Syst Pharmacol ; 13(3): 424-436, 2024 03.
Article in English | MEDLINE | ID: mdl-38243630

ABSTRACT

Model-informed precision dosing using virtual twins (MIPD-VTs) is an emerging strategy to predict target drug concentrations in clinical practice. Using a high virtualization MIPD-VT approach (Simcyp version 21), we predicted the steady-state clozapine concentration and clozapine dosage range to achieve a target concentration of 350 to 600 ng/mL in hospitalized patients with treatment-resistant schizophrenia (N = 11). We confirmed that high virtualization MIPD-VT can reasonably predict clozapine concentrations in individual patients with a coefficient of determination (R2 ) ranging between 0.29 and 0.60. Importantly, our approach predicted the final dosage range to achieve the desired target clozapine concentrations in 73% of patients. In two thirds of patients treated with fluvoxamine augmentation, steady-state clozapine concentrations were overpredicted two to four-fold. This work supports the application of a high virtualization MIPD-VT approach to inform the titration of clozapine doses in clinical practice. However, refinement is required to improve the prediction of pharmacokinetic drug-drug interactions, particularly with fluvoxamine augmentation.


Subject(s)
Antipsychotic Agents , Clozapine , Schizophrenia , Humans , Clozapine/pharmacokinetics , Clozapine/therapeutic use , Antipsychotic Agents/pharmacokinetics , Schizophrenia/drug therapy , Fluvoxamine , Schizophrenia, Treatment-Resistant
2.
CPT Pharmacometrics Syst Pharmacol ; 12(2): 168-179, 2023 02.
Article in English | MEDLINE | ID: mdl-36424701

ABSTRACT

Studies that focus on individual covariates, while ignoring their interactions, may not be adequate for model-informed precision dosing (MIPD) in any given patient. Genetic variations that influence protein synthesis should be studied in conjunction with environmental covariates, such as cigarette smoking. The aim of this study was to build virtual twins (VTs) of real patients receiving clozapine with interacting covariates related to genetics and environment and to delineate the impact of interacting covariates on predicted clozapine plasma concentrations. Clozapine-treated patients with schizophrenia (N = 42) with observed clozapine plasma concentrations, demographic, environmental, and genotype data were used to construct VTs in Simcyp. The effect of increased covariate virtualization was assessed by performing simulations under three conditions: "low" (demographic), "medium" (demographic and environmental interaction), and "high" (demographic and environmental/genotype interaction) covariate virtualization. Increasing covariate virtualization with interaction improved the coefficient of variation (R2 ) from 0.07 in the low model to 0.391 and 0.368 in the medium and high models, respectively. Whereas R2 was similar between the medium and high models, the high covariate virtualization model had improved accuracy, with systematic bias of predicted clozapine plasma concentration improving from -138.48 ng/ml to -74.65 ng/ml. A high level of covariate virtualization (demographic, environmental, and genotype) may be required for MIPD using VTs.


Subject(s)
Antipsychotic Agents , Clozapine , Schizophrenia , Humans , Clozapine/therapeutic use , Clozapine/adverse effects , Antipsychotic Agents/therapeutic use , Schizophrenia/drug therapy , Schizophrenia/genetics , Genotype
3.
Pharmacogenomics ; 23(15): 857-867, 2022 10.
Article in English | MEDLINE | ID: mdl-36169629

ABSTRACT

Pharmacogenomic (PGx) testing of cytochrome P450 (CYP) enzymes may improve the efficacy and/or safety of some medications. This is facilitated by increased availability and affordability of genotyping, the development of clinical practice PGx guidelines and regulatory support. However, the common occurrence of CYP phenoconversion, a mismatch between genotype-predicted CYP phenotype and the actual CYP phenotype, currently limits the application of PGx testing for precision dosing in psychiatry. This review proposes a stepwise approach to assist precision dosing in psychiatry via the introduction of PGx stewardship programs and innovative PGx education strategies. A future perspective on delivering precision dosing for psychiatrists is discussed that involves innovative clinical decision support systems powered by model-informed precision dosing.


Subject(s)
Decision Support Systems, Clinical , Psychiatry , Pharmacogenetics , Cytochrome P-450 CYP2D6/genetics , Cytochrome P-450 Enzyme System/genetics
4.
Front Psychiatry ; 12: 724170, 2021.
Article in English | MEDLINE | ID: mdl-34489765

ABSTRACT

Introduction: Polypharmacy and genetic variants that strongly influence medication response (pharmacogenomics, PGx) are two well-described risk factors for adverse drug reactions. Complexities arise in interpreting PGx results in the presence of co-administered medications that can cause cytochrome P450 enzyme phenoconversion. Aim: To quantify phenoconversion in a cohort of acute aged persons mental health patients and evaluate its impact on the reporting of medications with actionable PGx guideline recommendations (APRs). Methods: Acute aged persons mental health patients (N = 137) with PGx and medication data at admission and discharge were selected to describe phenoconversion frequencies for CYP2D6, CYP2C19 and CYP2C9 enzymes. The expected impact of phenoconversion was then assessed on the reporting of medications with APRs. Results: Post-phenoconversion, the predicted frequency at admission and discharge increased for CYP2D6 intermediate metabolisers (IMs) by 11.7 and 16.1%, respectively. Similarly, for CYP2C19 IMs, the predicted frequency at admission and discharge increased by 13.1 and 11.7%, respectively. Nineteen medications with APRs were prescribed 120 times at admission, of which 50 (42%) had APRs pre-phenoconversion, increasing to 60 prescriptions (50%) post-phenoconversion. At discharge, 18 medications with APRs were prescribed 122 times, of which 48 (39%) had APRs pre-phenoconversion, increasing to 57 prescriptions (47%) post-phenoconversion. Discussion: Aged persons mental health patients are commonly prescribed medications with APRs, but interpretation of these recommendations must consider the effects of phenoconversion. Adopting a collaborative care model between prescribers and clinical pharmacists should be considered to address phenoconversion and ensure the potential benefits of PGx are maximised.

5.
J Neural Transm (Vienna) ; 126(1): 5-18, 2019 Jan.
Article in English | MEDLINE | ID: mdl-30191366

ABSTRACT

Common polymorphisms in the genes encoding CYP2D6, CYP2C19, CYP2C9 and VKORC1 enzymes have an important role in predicting the occurrence of adverse effects and the efficacy of substrate medications. Drug-induced changes to the enzyme's phenotype, a process called phenoconversion, comprise another important factor contributing to interindividual variability in drug response. To date, there is lack of data on the frequency of these common polymorphisms and phenoconversion in the pan-ethnic Australian population. The aim of this study was to (1) describe allele, genotype and phenotype frequencies for CYP2D6, CYP2C19, CYP2C9 and VKORC1 enzymes in the pan-ethnic Australian population and (2) evaluate the frequency of actionable pharmacogenomic (PGx) variants and phenoconversion. Frequencies were calculated using the records of 5408 Australian patients (obtained from myDNA's propriety database), who were consecutively tested with the DNAdose PGx test which included the CYP2D6, CYP2C19, CYP2C9 and VKORC1 genes. In 2509 patients with listed medications at the time of testing, phenoconversion frequencies were calculated for CYP2D6, CYP2C19 and CYP2C9 enzymes. Allele, genotype and phenotype frequencies in our Australian patients correlated with a Caucasian population. Approximately 96% of patients had at least one actionable PGx variant. A five-fold increase in the frequency of poor metabolisers (PMs) for CYP2D6 and CYP2C19 was predicted by phenoconversion. Our study results indicate a high frequency of actionable PGx variants in our Australian population. With the addition of drug-induced phenoconversion, our results provide further support for the utilisation of PGx testing in clinical practice as another tool assisting prescribers in the application of personalised medicine.


Subject(s)
Cytochrome P-450 CYP2C19 , Cytochrome P-450 CYP2C9 , Cytochrome P-450 CYP2D6 , Drug-Related Side Effects and Adverse Reactions/enzymology , Drug-Related Side Effects and Adverse Reactions/genetics , Pharmacogenomic Variants , Precision Medicine , Vitamin K Epoxide Reductases , Adolescent , Adult , Aged , Aged, 80 and over , Australia , Child , Child, Preschool , Cytochrome P-450 CYP2C19/drug effects , Cytochrome P-450 CYP2C19/genetics , Cytochrome P-450 CYP2C9/drug effects , Cytochrome P-450 CYP2C9/genetics , Cytochrome P-450 CYP2D6/drug effects , Cytochrome P-450 CYP2D6/genetics , Drug Prescriptions , Female , Genotype , Humans , Infant , Male , Middle Aged , Phenotype , Polymorphism, Genetic , Vitamin K Epoxide Reductases/drug effects , Vitamin K Epoxide Reductases/genetics , Young Adult
6.
Ther Drug Monit ; 40(4): 495-502, 2018 08.
Article in English | MEDLINE | ID: mdl-29846282

ABSTRACT

BACKGROUND: Chemotherapy for colorectal, head and neck, and breast cancer continues to rely heavily on 5-fluorouracil and its oral prodrug capecitabine. Associations of serious fluoropyrimidine adverse effects have focused on inherited deficiency of the catabolic enzyme, dihydropyrimidine dehydrogenase. However, abnormal dihydropyrimidine dehydrogenase activity accounts for only about one-third of observed toxicity cases. Thus, the cause of most fluorouracil toxicity cases remains unexplained. METHODS: For this small cohort study, thymine (THY) 250 mg was administered orally to 6 patients who had experienced severe toxicity during treatment with 5FU or capecitabine. Plasma and urine were analyzed for THY and its catabolites dihydrothymine (DHT) and ß-ureidoisobutyrate. RESULTS: Of the 6 patients, 2 had decreased THY elimination and raised urinary THY recovery consistent with inherited partial dihydropyrimidine dehydrogenase deficiency, confirmed by DPYD sequencing. Unexpectedly, 3 patients displayed grossly raised plasma THY concentrations but normal elimination profiles (compared with a normal range for healthy volunteers previously published by the authors). DPYD and DPYS sequencing of these 3 patients did not reveal any significant loss-of-activity allelic variants. The authors labeled the phenotype in these 3 patients as "enhanced thymine absorption". Only 1 of the 6 cases of toxicity had a normal postdose plasma profile for THY and its catabolites. Postdose urine collections from all 6 patients had THY/DHT urinary ratios above 4.0, clearly separated from the ratios in healthy subjects that were all below 3.0. CONCLUSIONS: This small cohort provided evidence for a hypothesis that fluorouracil toxicity cases may include a previously undescribed pyrimidine absorption variant, "enhanced thymine absorption," and elevated THY/DHT ratios in urine may predict fluorouracil toxicity. A prospective study is currently being conducted.


Subject(s)
Thymine/pharmacokinetics , Adult , Aged , Amidohydrolases/genetics , Capecitabine/adverse effects , Dihydrouracil Dehydrogenase (NADP)/genetics , Female , Fluorouracil/adverse effects , Humans , Male , Middle Aged , Neoplasms/blood , Neoplasms/urine , Phenotype , Thymine/analogs & derivatives , Thymine/blood , Thymine/urine
7.
Genet Med ; 19(12): 1346-1355, 2017 12.
Article in English | MEDLINE | ID: mdl-28661491

ABSTRACT

PurposePopulation-based carrier screening for fragile X syndrome (FXS) is still not universally endorsed by professional organizations due to concerns around genetic counseling for complex information and potential for psychosocial harms.MethodsWe determined uptake levels, decision making, and psychosocial impact in a prospective study of pregnant and nonpregnant Australian women offered FXS carrier screening in clinical settings. Women received pretest genetic counseling, and completed questionnaires when deciding and one month later.ResultsOf 1,156 women recruited, 83.1% returned the first questionnaire with 70.6% nonpregnant and 58.8% pregnant women choosing testing (χ2=16.98, P<0.001). Overall, informed choice was high in both nonpregnant (77.4%) and pregnant (72.9%) women (χ2=0.21, P=0.644), and more tested (76.0%) than not-tested (66.7%) women (χ2=6.35, P=0.012) made an informed choice. Measures of depression, stress, and anxiety were similar to population norms for ~85% of women. Decisional conflict and regret were generally low; however, decisional uncertainty and regret were greater in pregnant than nonpregnant women, and not-tested than tested women (uncertainty: χ2=18.51, P<0.001 and χ2=43.11, P<0.001, respectively; regret: χ2=6.61, P<0.037 and χ2=35.54, P<0.001, respectively).ConclusionWe provide evidence to inform guidelines that population FXS carrier screening can be implemented with minimal psychosocial harms following appropriate information and prescreening genetic counseling.


Subject(s)
Decision Making , Fragile X Syndrome/epidemiology , Heterozygote , Adolescent , Adult , Aged , Choice Behavior , Female , Fragile X Syndrome/diagnosis , Fragile X Syndrome/genetics , Fragile X Syndrome/psychology , Genetic Testing , Humans , Mass Screening , Middle Aged , Population Surveillance , Pregnancy , Psychology , Surveys and Questionnaires , Young Adult
8.
Am J Hum Genet ; 91(2): 252-64, 2012 Aug 10.
Article in English | MEDLINE | ID: mdl-22840365

ABSTRACT

We previously reported on nonrecurrent overlapping duplications at Xp11.22 in individuals with nonsyndromic intellectual disability (ID) harboring HSD17B10, HUWE1, and the microRNAs miR-98 and let-7f-2 in the smallest region of overlap. Here, we describe six additional individuals with nonsyndromic ID and overlapping microduplications that segregate in the families. High-resolution mapping of the 12 copy-number gains reduced the minimal duplicated region to the HUWE1 locus only. Consequently, increased mRNA levels were detected for HUWE1, but not HSD17B10. Marker and SNP analysis, together with identification of two de novo events, suggested a paternally derived intrachromosomal duplication event. In four independent families, we report on a polymorphic 70 kb recurrent copy-number gain, which harbors part of HUWE1 (exon 28 to 3' untranslated region), including miR-98 and let-7f-2. Our findings thus demonstrate that HUWE1 is the only remaining dosage-sensitive gene associated with the ID phenotype. Junction and in silico analysis of breakpoint regions demonstrated simple microhomology-mediated rearrangements suggestive of replication-based duplication events. Intriguingly, in a single family, the duplication was generated through nonallelic homologous recombination (NAHR) with the use of HUWE1-flanking imperfect low-copy repeats, which drive this infrequent NAHR event. The recurrent partial HUWE1 copy-number gain was also generated through NAHR, but here, the homologous sequences used were identified as TcMAR-Tigger DNA elements, a template that has not yet been reported for NAHR. In summary, we showed that an increased dosage of HUWE1 causes nonsyndromic ID and demonstrated that the Xp11.22 region is prone to recombination- and replication-based rearrangements.


Subject(s)
Chromosomes, Human, X/genetics , DNA Copy Number Variations/genetics , Gene Rearrangement/genetics , Intellectual Disability/genetics , Ubiquitin-Protein Ligases/genetics , Chromosome Mapping , Chromosomes, Artificial, Bacterial/genetics , Comparative Genomic Hybridization , Computational Biology , DNA Replication/genetics , Gene Duplication/genetics , Humans , Pedigree , Polymerase Chain Reaction , Polymorphism, Single Nucleotide/genetics , Recombination, Genetic/genetics , Tumor Suppressor Proteins
9.
Per Med ; 8(4): 397-400, 2011 Jul.
Article in English | MEDLINE | ID: mdl-29783332

ABSTRACT

GenesFX Health (Melbourne, Australia) is providing genetic testing with clinical interpretation to personalize how people take medications. The company's aim is to achieve the best health outcomes for patients by ensuring that the way they metabolize medications is included when doctors prescribe them medication. This would be achieved by introducing pharmacogenomics into medical practice to provide more informed prescribing, reduce side effects and create maximum efficacy of medications. Through the use of GenesFX Health innovative genetic test, DNAdose®, GenesFX Health is able to analyze the profile of a patient's genetic variation and maps this to the optimum drug and dosage for a specific treatment. The company's focus on the interpretation of genetic test results has led to the development of a Pharmacogenomic Database and Pharmacogenomic Interpretation System, which allows the team to communicate complex genetic test results in a meaningful way to doctors. There is a significant opportunity to expand GenesFX Health current model of delivering pharmacogenomic tests, by partnering with other laboratories around the world, making pharmacogenomics more accessible and clinically useful. Doctors using the service have welcomed the clinical guidance. Patients have felt relieved and empowered by understanding why they have adverse reactions to medications, and which medications and doses are most suited to them.

10.
Prenat Diagn ; 30(6): 522-30, 2010 Jun.
Article in English | MEDLINE | ID: mdl-20509151

ABSTRACT

OBJECTIVES: To map prenatal screening and diagnostic testing pathways in Victorian pregnant women during 2003 to 2004; measure the impact of prenatal diagnostic testing uptake on the effectiveness of prenatal screening for Down syndrome; and assess factors influencing uptake of diagnostic testing following screening. METHODS: State-wide data collections of prenatal screening and diagnostic tests were linked to all Victorian births and pregnancy terminations for birth defects. RESULTS: Overall, 52% of women had a prenatal test (65 692/126 305); screening (44.9%), diagnostic testing (3.9%), or both (3.2%). Uptake of diagnostic testing was 71.4% (2390/3349) after an increased risk screen result, and 2.5% (1381/54 286) after a low risk result. Variation in uptake of diagnostic testing reduced the effectiveness of the screening program by 11.2%: from 87.4% (sensitivity - 125/143) to 76.2% (prenatal diagnoses of Down syndrome - 109/143). In both the increased and low risk groups, uptake was influenced by absolute numerical risk, as well as by the change in numerical risk from a priori risk. CONCLUSIONS: This comprehensive follow-up demonstrates clearly that numerical risk is being used to aid in decision making about confirmatory diagnostic testing. Collectively, these fundamental individual decisions will impact on the overall effectiveness of screening programmes for Down syndrome.


Subject(s)
Down Syndrome/diagnosis , Mass Screening/methods , Prenatal Diagnosis/methods , Prenatal Diagnosis/statistics & numerical data , Program Evaluation , Abortion, Induced/statistics & numerical data , Adult , Algorithms , Chromosomes, Human, Pair 18 , Decision Making , Down Syndrome/epidemiology , Female , Humans , Mass Screening/statistics & numerical data , Pregnancy , Trisomy/diagnosis , Victoria/epidemiology
11.
Clin Biochem Rev ; 30(2): 55-65, 2009 May.
Article in English | MEDLINE | ID: mdl-19565025

ABSTRACT

Pharmacogenomics is a new field where testing an individual can define either a risk status for an adverse event, or the rate of metabolism of a drug. This is achieved by the categorisation of the enzyme activity or documenting genetic polymorphisms of a metabolising enzyme. The best example of risk status assessment is the recent finding that HLA-B typing a person can predict whether they are at risk of a severe skin reaction from the drug abacavir. Those patients showing HLA-B*5701, who are being considered for abacavir therapy, can be prevented from developing potentially toxic epidermal necrosis (TEN) or Stevens-Johnson Syndrome by avoiding abacavir. The evidence for HLA-B typing for allopurinol and carbamazepine has also been described. Most other pharmacogenomic tests are of drug metabolising enzymes, which can either be assessed using "probe" drugs and measuring a ratio of parent drug to metabolite, or, by genetic testing for polymorphisms of the genes. In practice, testing is usually done by molecular testing, but this typically does not detect all polymorphisms. This article briefly reviews the evidence for the utilisation of pharmacogenomics for antidepressant drugs, tamoxifen, codeine, warfarin, azathioprine, clopidogrel, omeprazole, tacrolimus and irinotecan. There are few pharmacogenomics tests being carried out in practice, as there has not been a wide appreciation of their use, and only limited evidence exists for many individual drugs. It is expected that utilisation will increase as more evidence becomes available and there is a wider understanding of the existing evidence by the medical profession.

12.
Pharmacogenomics ; 10(7): 1091-9, 2009 Jul.
Article in English | MEDLINE | ID: mdl-19604082

ABSTRACT

Thiopurine methyltransferase genotyping and thiopurine metabolite testing has been established as an adjunct to monitoring patients taking thiopurine drugs. This special report describes the clinical implications for this type of testing for patients with inflammatory bowel disease who are taking thiopurine drugs. A total of 10% of patients were found to be intermediate metabolizers and the mean dosage (in mg/kg equivalent) was lower in intermediate metabolizers than extensive metabolizers. The metabolite levels did not correlate with scores measuring clinical severity but levels of 6-methylmercaptopurine were related to the dosage of the drugs. Despite considerable study of thiopurine methyltransferase testing in the literature, it is still not widely used in many geographical areas. This study adds to the evidence about using such testing as well as expanding the role of simultaneously measuring thiopurine metabolites. Further work is planned to evaluate the uptake when such testing becomes available locally as a clinical service.


Subject(s)
Inflammatory Bowel Diseases/enzymology , Inflammatory Bowel Diseases/genetics , Mercaptopurine/metabolism , Mercaptopurine/therapeutic use , Methyltransferases/genetics , Methyltransferases/metabolism , Adolescent , Adult , Aged , Aged, 80 and over , Cross-Sectional Studies , Genetic Testing/methods , Humans , Inflammatory Bowel Diseases/drug therapy , Middle Aged , Young Adult
13.
Epilepsia ; 50(7): 1689-96, 2009 Jul.
Article in English | MEDLINE | ID: mdl-19453704

ABSTRACT

PURPOSE: The association between a specific polymorphism (3435C>T) in the ABCB1 gene, coding for the membrane drug transporter P-glycoprotein (PgP), and pharmacoresistance to seizure control is controversial. Studies have been limited by multiple drug use, chronic cohorts with varying definitions, and retrospective clinical data. Herein we examine the relationship of this polymorphism with seizure recurrence in three independent international cohorts of patients newly treated for epilepsy. METHODS: Data were collected on demographics, medication details, and seizure control after 12 months of treatment. The distribution of ABCB1 3435C>T genotypes was compared between patients with and without recurrent unprovoked seizures. RESULTS: Five hundred forty-two newly treated patients were enrolled (212 from Australia, 285 from Scotland, and 45 from Hong Kong). A total of 38.4% had recurrent unprovoked seizures after starting antiepileptic drug (AED) treatment. Genotype frequencies and ethnicity did not differ between the Scottish and Australian cohorts, but both were significantly different in the Hong Kong cohort. There was no significant relationship between the ABCB1 3435C>T genotype and the rate of recurrence of unprovoked seizures in the three cohorts individually or combined; however the epilepsy syndrome and a greater number of seizures pretreatment was associated with an increased risk of seizure recurrence. CONCLUSIONS: The ABCB1 3435C>T genotype does not have a major role in determining the efficacy of seizure control with initial AED therapy. The study highlights issues that arise in combining pharmacogenetic datasets from different ethnic regions and health systems, an approach that is essential to advance this field.


Subject(s)
ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics , Anticonvulsants/therapeutic use , Drug Resistance, Multiple/genetics , Epilepsy/drug therapy , Epilepsy/genetics , ATP Binding Cassette Transporter, Subfamily B , Adult , Asian People/genetics , Australia/ethnology , Cohort Studies , Epilepsy/ethnology , Female , Genotype , Hong Kong/ethnology , Humans , Male , Middle Aged , Pharmacogenetics , Polymorphism, Single Nucleotide/genetics , Recurrence , Scotland/ethnology , White People/genetics
14.
Eur J Hum Genet ; 17(1): 66-70, 2009 Jan.
Article in English | MEDLINE | ID: mdl-18665196

ABSTRACT

The uptake of predictive testing for Huntington disease informs our understanding of decision making by those at risk and assists with planning for service provision. Uptake figures have been reported from several centers based on the total number of people who have undertaken predictive testing as a percentage of those estimated to be at 50% risk in the region. This method produced a figure of 35% from our own service, much higher than observation of the local pedigrees indicated, and higher than other published reports. We have identified some errors in the commonly used formula. The major errors are the use of the cumulative total of those who have had testing with a static denominator of those at 50% risk, and the failure to exclude from the at-risk group those who are too young and therefore ineligible to test.We report data from the Huntington Disease Register of Victoria and estimate the prevalence to be 8 per 100,000 in 1999. Additional data on individuals at risk were collated. We found that for every diagnosed person there were 4.2 individuals at 50% risk, a lower ratio than one to five hypothesized in the literature. We examined these ratios in the context of uptake.Significantly, we provide a solution to the calculation of uptake with a formula that factors in a dynamic denominator and corrects for the number of years testing has been offered. Using this formula, we calculated an uptake of 13.0-15.4% for the state of Victoria, Australia. This formula can be used to compare uptake across different centers.


Subject(s)
Genetic Testing , Huntington Disease/diagnosis , Huntington Disease/genetics , Age Factors , Humans , Huntington Disease/epidemiology , Registries , Risk Assessment , Victoria/epidemiology
15.
Pharmacogenet Genomics ; 19(2): 147-52, 2009 Feb.
Article in English | MEDLINE | ID: mdl-19077679

ABSTRACT

OBJECTIVES: Most pharmacogenomic studies have attempted to identify single nucleotide polymorphism (SNP) markers that are predictive for treatment outcomes. It is, however, unlikely in complex diseases such as epilepsy, affecting heterogeneous populations, that a single SNP will adequately explain treatment outcomes. This study reports an approach to develop a multi-SNP model to classify treatment outcomes for such a disease and compares this with single-SNP models. METHODS: A prospectively collected dataset of outcomes in 115 patients newly treated for epilepsy, with genotyping for 4041 SNPs in 279 candidate genes, was used for the model development. A cross-validation-based methodology identified SNPs most influential in predicting seizure control after 1 year of drug treatment and then incorporated these into a multi-SNP classification model; using the k-Nearest Neighbour (kNN) supervised learning approach. The classifier was cross-validated to determine its effectiveness in predicting treatment outcome in the developmental cohort and then in two independent validation cohorts. In each, the classification by the multi-SNP model was compared with that of models using the individual SNPs alone. RESULTS: Five SNPs were selected for the multi-SNP model. Cross-validation showed that the multi-SNP model had a predictive accuracy of 83.5% in the developmental cohort and sensitivity and positive predictive values above 80% in both the independent validation cohorts. In all cases, the multi-SNP model classified the treatment outcomes better than those using any individual SNPs alone. CONCLUSION: The results show that a classifier using multiple SNPs can predict treatment outcome more reliably than single-SNP models. This multi-SNP classifier should be tested on data from newly diagnosed epilepsy populations to determine its broad clinical validity. Our method to developing a multi-SNP classifier could be applied to pharmacogenomic studies of other complex diseases.


Subject(s)
Pharmacogenetics/methods , Polymorphism, Single Nucleotide , Algorithms , Anticonvulsants/therapeutic use , Cohort Studies , Epilepsy/drug therapy , Epilepsy/genetics , Genetic Predisposition to Disease , Genotype , Humans , Models, Statistical
16.
Genet Med ; 10(7): 525-35, 2008 Jul.
Article in English | MEDLINE | ID: mdl-18580686

ABSTRACT

PURPOSE: To develop a model of offering population carrier screening for fragile X syndrome to nonpregnant women in primary care, using a program evaluation framework. METHODS: A three-phase approach included: (I) needs assessment exploring staff and client attitudes, and informing development of educational materials, questionnaires and protocols; (II) offering screening to women, with questionnaires at baseline (Q1) and another (Q2) 1-month later; (III) genetic counseling for test-positive women and interviews with a subgroup of participants. RESULTS: Of 338 volunteering for Phase II, 94% completed Q1, 59% completed Q2, and 20% (N = 65) chose testing revealing one premutation carrier and three gray zone results; 31 women were interviewed. Tested women had more positive attitudes toward screening (Q1: P < 0.001; Q2: P < 0.001) compared with untested, although there was no significant difference in mean knowledge scores or anxiety. Women generally supported being offered prepregnancy screening; however, reasons against being tested included: not currently planning a family; perceiving benefits of screening as unimportant; and having to return for testing. CONCLUSION: This is the first prospective study exploring informed decision-making for fragile X syndrome carrier screening, using a thorough process of consultation, with no apparent harms identified. It provides a model for development of future genetic screening programs.


Subject(s)
Fragile X Syndrome/genetics , Genetic Carrier Screening/methods , Genetic Testing/methods , Adult , Blotting, Southern , DNA Primers/genetics , Female , Health Knowledge, Attitudes, Practice , Humans , Interviews as Topic , Pilot Projects , Prospective Studies , Victoria
17.
Lancet Neurol ; 6(11): 970-80, 2007 Nov.
Article in English | MEDLINE | ID: mdl-17913586

ABSTRACT

BACKGROUND: The Epilepsy Genetics (EPIGEN) Consortium was established to undertake genetic mapping analyses with augmented statistical power to detect variants that influence the development and treatment of common forms of epilepsy. METHODS: We examined common variations across 279 prime candidate genes in 2717 case and 1118 control samples collected at four independent research centres (in the UK, Ireland, Finland, and Australia). Single nucleotide polymorphism (SNP) and combined set-association analyses were used to examine the contribution of genetic variation in the candidate genes to various forms of epilepsy. FINDINGS: We did not identify clear, indisputable common genetic risk factors that contribute to selected epilepsy subphenotypes across multiple populations. Nor did we identify risk factors for the general all-epilepsy phenotype. However, set-association analysis on the most significant p values, assessed under permutation, suggested the contribution of numerous SNPs to disease predisposition in an apparent population-specific manner. Variations in the genes KCNAB1, GABRR2, KCNMB4, SYN2, and ALDH5A1 were most notable. INTERPRETATION: The underlying genetic component to sporadic epilepsy is clearly complex. Results suggest that many SNPs contribute to disease predisposition in an apparently population-specific manner. However, subtle differences in phenotyping across cohorts, combined with a poor understanding of how the underlying genetic component to epilepsy aligns with current phenotypic classifications, might also account for apparent population-specific genetic risk factors. Variations across five genes warrant further study in independent cohorts to clarify the tentative association.


Subject(s)
Chromosome Mapping , Epilepsy/genetics , Seizures/genetics , Adult , Case-Control Studies , Cohort Studies , Genetic Predisposition to Disease , Genetic Variation , Genotype , Humans , Kv1.3 Potassium Channel/genetics , Large-Conductance Calcium-Activated Potassium Channel beta Subunits/genetics , Nerve Tissue Proteins/genetics , Phenotype , Polymorphism, Single Nucleotide , Receptors, GABA-A , Receptors, GABA-B/genetics , Succinate-Semialdehyde Dehydrogenase/genetics , Synapsins/genetics , Syndrome
18.
Genet Med ; 8(11): 673-80, 2006 Nov.
Article in English | MEDLINE | ID: mdl-17108758

ABSTRACT

PURPOSE: This retrospective study describes 15 years of experience in predictive testing for Huntington disease at a single center in Victoria, Australia. METHOD: Data collected on 756 participants included age, gender, family history, prior risk and the age at which this risk became known, exposure to Huntington disease, number of children, and proximity to the testing center. RESULTS: Some 57.8% of participants were female, and 88.8% had a 50% risk of developing Huntington disease. The mean age at entry was 40.4 years and was gender-independent. Of all completed tests (n = 648), 37.5% gave high-risk results, and 3.2% were in the zone of reduced penetrance. The 14.3% who withdrew from testing tended to be younger and childless, lacked exposure to severe Huntington disease, and more often at 25% or less risk. Some 32.4% of candidates presented for testing within 1 year of becoming aware of their risk, and most of these individuals had little or no exposure to severe Huntington disease. Those whose exposure was considerable waited on average for more than 13 years. Among the most inexperienced candidates were a group of "adoptees" (raised away from their biological family). Maternal transmission was the source of risk for 19 of 20 adoptees. CONCLUSION: This study illustrates the significance of exposure to Huntington disease and its impact on the timing of testing.


Subject(s)
Genetic Testing , Huntington Disease/diagnosis , Adolescent , Adoption , Adult , Aged , Aged, 80 and over , Australia , Child , Family Health , Female , Genetic Linkage , Genetic Testing/methods , Humans , Huntington Disease/genetics , Male , Middle Aged , Pregnancy , Prognosis , Retrospective Studies , Risk Factors
19.
J Med Screen ; 13(1): 8-13, 2006.
Article in English | MEDLINE | ID: mdl-16569299

ABSTRACT

OBJECTIVES: The Genetic Health Services Victoria maternal serum screening (MSS) quadruple test has been available to pregnant women in Victoria since 1996. The objectives of this study were to follow up the pregnancies screened by MSS between July 1998 and June 2000 and to determine the performance characteristics of the test for Down's syndrome, trisomy 18 and neural tube defects (NTDs). METHODS: MSS results were matched to pregnancy outcome information from the Perinatal Data Collection Unit and Birth Defects Register, using automated probabilistic record linkage. For unmatched pregnancies, manual follow-up was carried out by contacting referring doctors and hospitals, resulting in a very high follow-up rate of 99.2% (18,989/19,143). RESULTS: The sensitivity of MSS for Down's syndrome was 85% (23/27-95%CI 72-99%) with a falsepositive rate (FPR) of 6.8% (risk threshold >or= 1 in 250). While using a fixed 5% FPR, the sensitivity for Down's syndrome was slightly lower (78%). The sensitivity for trisomy 18 was 44% (4/9 - 95% CI 12-77%) with a FPR of 0.5% (risk threshold of >or= 1 in 200). 11 of the 15 (73 - 95%CI 51-97%) cases of open NTDs were detected from screening, with a 1% FPR (risk threshold alpha-fetoprotein [AFP] >or=2.5 MoM). All cases of anencephaly had increased AFP levels. CONCLUSION: Probabilistic record linkage and manual follow-up is an efficient method for ascertainment of pregnancy outcomes, with a higher follow-up rate than that reported in similar studies. MSS should remain an available option for all pregnant women in Victoria, with test characteristics comparable with other recent reports of the quadruple test.


Subject(s)
Chromosomes, Human, Pair 18 , Down Syndrome/diagnosis , Neural Tube Defects/diagnosis , Trisomy/diagnosis , Adult , False Positive Reactions , Female , Follow-Up Studies , Humans , Mass Screening , Models, Statistical , Pregnancy , Pregnancy Outcome , Prenatal Diagnosis , Probability , Records , Reproducibility of Results , Risk , Sensitivity and Specificity , Victoria , alpha-Fetoproteins/metabolism
20.
Prenat Diagn ; 25(8): 656-64, 2005 Aug.
Article in English | MEDLINE | ID: mdl-16049990

ABSTRACT

OBJECTIVES: Informed choice for prenatal screening has long been considered an essential aspect of service provision, and has been researched extensively in the second trimester. This study aims at examining whether women having first-trimester screening in a private clinic had made an informed choice. METHODS: A cross-sectional survey recruited women having first-trimester screening at specialist ultrasound practices. Two questionnaires containing a validated Multidimensional Measure of Informed Choice (MMIC) were self-administered pre- and post-screening. RESULTS: MMIC was completed by 81% (163/202) of women. Ninety-nine percent of women had a positive attitude towards screening, therefore informed choice was essentially measured on knowledge alone. Pre-screening, 68% made an informed choice, compared with 74% post-screening (chi2 = 1.6, p = 0.21 (McNemar)). Knowledge was associated with education level, information sources and perception of screening as routine or optional. CONCLUSIONS: The Australasian Guidelines on prenatal screening state that all women having testing should be provided with written information, and it should be ensured that they have appropriate understanding of the test(s). These guidelines are not being met, even in private clinical care. Health professionals should ensure that all women are provided with suitable information about prenatal screening that is tailored to their level of education and individual needs, and should emphasise that screening is optional.


Subject(s)
Choice Behavior , Down Syndrome/diagnosis , Informed Consent , Mass Screening/psychology , Prenatal Diagnosis/psychology , Adult , Cross-Sectional Studies , Educational Status , Female , Humans , Pregnancy , Pregnancy Trimester, First , Surveys and Questionnaires , Victoria
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